dorsal/arxiv
View SchemaRotational friction on small globular proteins: Combined dielectric and hydrodynamic effect
| Authors | Arnab Mukherjee, Biman Bagchi |
|---|---|
| Categories | |
| ArXiv ID | physics/0408071 |
| URL | https://arxiv.org/abs/physics/0408071 |
| DOI | 10.1016/j.cplett.2005.01.125 |
Abstract
Rotational friction on proteins and macromolecules is known to derive contributions from at least two distinct sources -- hydrodynamic (due to viscosity) and dielectric friction (due to polar interactions). In the existing theoretical approaches, the effect of the latter is taken into account in an {\it ad hoc} manner, by increasing the size of the protein with the addition of a hydration layer. Here we calculate the rotational dielectric friction on a protein ($\zeta_{DF}$) by using a generalized arbitrary charge distribution model (where the charges are obtained from quantum chemical calculation) and the hydrodynamic friction with stick boundary condition, ($\zeta_{hyd}^{stick}$) by using the sophisticated theoretical technique known as tri-axial ellipsoidal method, formulated by Harding [S. E. Harding, Comp. Biol. Med. {\bf 12}, 75 (1982)]. The calculation of hydrodynamic friction is done with only the dry volume of the protein (no hydration layer). We find that the total friction obtained by summing up $\zeta_{DF}$ and $\zeta_{hyd}^{stick}$ gives reasonable agreement with the experimental results, i.e., $\zeta_{exp} \approx \zeta_{DF} + \zeta_{hyd}^{stick}$.
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"abstract": "Rotational friction on proteins and macromolecules is known to derive\ncontributions from at least two distinct sources -- hydrodynamic (due to\nviscosity) and dielectric friction (due to polar interactions). In the existing\ntheoretical approaches, the effect of the latter is taken into account in an\n{\\it ad hoc} manner, by increasing the size of the protein with the addition of\na hydration layer. Here we calculate the rotational dielectric friction on a\nprotein ($\\zeta_{DF}$) by using a generalized arbitrary charge distribution\nmodel (where the charges are obtained from quantum chemical calculation) and\nthe hydrodynamic friction with stick boundary condition,\n($\\zeta_{hyd}^{stick}$) by using the sophisticated theoretical technique known\nas tri-axial ellipsoidal method, formulated by Harding [S. E. Harding, Comp.\nBiol. Med. {\\bf 12}, 75 (1982)]. The calculation of hydrodynamic friction is\ndone with only the dry volume of the protein (no hydration layer). We find that\nthe total friction obtained by summing up $\\zeta_{DF}$ and\n$\\zeta_{hyd}^{stick}$ gives reasonable agreement with the experimental results,\ni.e., $\\zeta_{exp} \\approx \\zeta_{DF} + \\zeta_{hyd}^{stick}$.",
"arxiv_id": "physics/0408071",
"authors": [
"Arnab Mukherjee",
"Biman Bagchi"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph"
],
"doi": "10.1016/j.cplett.2005.01.125",
"title": "Rotational friction on small globular proteins: Combined dielectric and hydrodynamic effect",
"url": "https://arxiv.org/abs/physics/0408071"
},
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